UniProtKB - Q04491 (SEC13_YEAST)
Protein transport protein SEC13
SEC13
Functioni
Functions as a component of the nuclear pore complex (NPC) and the COPII coat. It is one of 5 proteins constituting the COPII coat, which is involved in anterograde (ER to Golgi) double-membrane transport vesicle formation. First the small GTPase SAR1, activated by and binding to the integral ER membrane protein SEC12, exchanges GDP for GTP and recruits the heterodimer SEC23/24, which in turn recruits the heterotetramer SEC13-SEC31. The polymerization of COPII coat complexes then causes physically the deformation (budding) of the membrane, leading to the creation of a transport vesicle. The COPII complex is dissociated upon SAR1-GTP hydrolysis to SAR1-GDP. SEC23 functions as the SAR1 GTPase activating protein, whose activity is stimulated in the presence of SEC13/31. SEC13 is directly or indirectly required for normal ER membrane and nuclear envelope morphology. It also functions as a component of the nuclear pore complex (NPC). NPC components, collectively referred to as nucleoporins (NUPs), can play the role of both NPC structural components and of docking or interaction partners for transiently associated nuclear transport factors. SEC13 is required for efficient mRNA export from the nucleus to the cytoplasm and for correct nuclear pore biogenesis and distribution. Component of the SEA complex which coats the vacuolar membrane and is involved in intracellular trafficking, autophagy, response to nitrogen starvation, and amino acid biogenesis.
20 PublicationsMiscellaneous
GO - Molecular functioni
- structural molecule activity Source: SGD
GO - Biological processi
- COPII-coated vesicle budding Source: SGD
- mRNA transport Source: UniProtKB-KW
- nuclear pore localization Source: SGD
- positive regulation of ER to Golgi vesicle-mediated transport Source: ComplexPortal
- positive regulation of GTPase activity Source: SGD
- positive regulation of protein exit from endoplasmic reticulum Source: ComplexPortal
- positive regulation of TORC1 signaling Source: SGD
- positive regulation of TOR signaling Source: GO_Central
- positive regulation of transcription, DNA-templated Source: SGD
- protein exit from endoplasmic reticulum Source: GO_Central
- protein import into nucleus Source: GO_Central
- regulation of TORC1 signaling Source: ComplexPortal
- ubiquitin-dependent ERAD pathway Source: SGD
Keywordsi
Biological process | ER-Golgi transport, mRNA transport, Protein transport, Translocation, Transport |
Enzyme and pathway databases
Reactomei | R-SCE-204005, COPII-mediated vesicle transport R-SCE-3232142, SUMOylation of ubiquitinylation proteins R-SCE-4085377, SUMOylation of SUMOylation proteins R-SCE-4551638, SUMOylation of chromatin organization proteins R-SCE-4570464, SUMOylation of RNA binding proteins |
Names & Taxonomyi
Protein namesi | Recommended name: Protein transport protein SEC13 |
Gene namesi | Name:SEC13 Synonyms:ANU3 Ordered Locus Names:YLR208W ORF Names:L8167.4 |
Organismi | Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) |
Taxonomic identifieri | 559292 [NCBI] |
Taxonomic lineagei | Eukaryota › Fungi › Dikarya › Ascomycota › Saccharomycotina › Saccharomycetes › Saccharomycetales › Saccharomycetaceae › Saccharomyces › |
Proteomesi |
|
Organism-specific databases
SGDi | S000004198, SEC13 |
VEuPathDBi | FungiDB:YLR208W |
Subcellular locationi
Endoplasmic reticulum
Nucleus
- nuclear pore complex 1 Publication
Vacuole
Other locations
Endoplasmic reticulum
- endoplasmic reticulum Source: ComplexPortal
- endoplasmic reticulum membrane Source: UniProtKB-SubCell
Nucleus
- nuclear pore outer ring Source: SGD
Vacuole
- vacuolar membrane Source: UniProtKB-SubCell
Other locations
- cell periphery Source: SGD
- COPII vesicle coat Source: SGD
- Seh1-associated complex Source: SGD
Keywords - Cellular componenti
Cytoplasmic vesicle, Endoplasmic reticulum, Membrane, Nuclear pore complex, Nucleus, VacuolePathology & Biotechi
Mutagenesis
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Mutagenesisi | 176 | G → R: Leads to mislocalization of NPCs and overproliferation of the nuclear and ER membranes at 34 degree Celsius. 1 Publication | 1 | |
Mutagenesisi | 224 | S → K: Growth inhibited above 30 degrees Celsius. 1 Publication | 1 | |
Mutagenesisi | 262 | W → R: Growth inhibited above 30 degrees Celsius. 1 Publication | 1 | |
Mutagenesisi | 266 | G → D: Growth inhibited above 34 degrees Celsius. 1 Publication | 1 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
ChainiPRO_0000051206 | 1 – 297 | Protein transport protein SEC13Add BLAST | 297 |
Proteomic databases
MaxQBi | Q04491 |
PaxDbi | Q04491 |
PRIDEi | Q04491 |
PTM databases
iPTMneti | Q04491 |
Interactioni
Subunit structurei
The basic repeat unit of a COPII coated vesicle is composed of 5 proteins: the small GTPase SAR1, the heterodimeric SEC23-SEC24 complex, and the heterotetrameric SEC13-SEC31 complex. This repeat unit polymerizes to induce membrane deformation into a transport vesicle.
Component of the nuclear pore complex (NPC). NPC constitutes the exclusive means of nucleocytoplasmic transport. NPCs allow the passive diffusion of ions and small molecules and the active, nuclear transport receptor-mediated bidirectional transport of macromolecules such as proteins, RNAs, ribonucleoparticles (RNPs), and ribosomal subunits across the nuclear envelope. Due to its 8-fold rotational symmetry, all subunits are present with 8 copies or multiples thereof. SEC13 is part of the heptameric 0.5 MDa autoassembling NUP84 NPC subcomplex (NUP84, NUP85, NUP120, NUP133, NUP145C, SEC13 and SEH1).
Component of the SEA complex composed of at least IML1/SEA1, RTC1/SEA2, MTC5/SEA3, NPR2, NPR3, SEA4, SEC13 and SEH1.
5 PublicationsBinary interactionsi
Q04491
With | #Exp. | IntAct |
---|---|---|
MTC5 [Q03897] | 5 | EBI-16529,EBI-32422 |
NUP145 [P49687] | 24 | EBI-16529,EBI-11730 |
SEC31 [P38968] | 6 | EBI-16529,EBI-20524 |
Protein-protein interaction databases
BioGRIDi | 31476, 301 interactors |
ComplexPortali | CPX-2523, COPII vesicle coat complex CPX-3231, SEA complex CPX-824, Nuclear pore complex |
DIPi | DIP-1826N |
IntActi | Q04491, 30 interactors |
MINTi | Q04491 |
STRINGi | 4932.YLR208W |
Miscellaneous databases
RNActi | Q04491, protein |
Structurei
Secondary structure
3D structure databases
SMRi | Q04491 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | Q04491 |
Family & Domainsi
Domains and Repeats
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Repeati | 7 – 46 | WD 1Add BLAST | 40 | |
Repeati | 51 – 92 | WD 2Add BLAST | 42 | |
Repeati | 97 – 138 | WD 3Add BLAST | 42 | |
Repeati | 143 – 195 | WD 4Add BLAST | 53 | |
Repeati | 202 – 244 | WD 5Add BLAST | 43 | |
Repeati | 252 – 291 | WD 6Add BLAST | 40 |
Sequence similaritiesi
Keywords - Domaini
Repeat, WD repeatPhylogenomic databases
eggNOGi | KOG1332, Eukaryota |
GeneTreei | ENSGT00940000153393 |
HOGENOMi | CLU_032441_0_1_1 |
InParanoidi | Q04491 |
OMAi | TVDTGHE |
Family and domain databases
Gene3Di | 2.130.10.10, 1 hit |
InterProi | View protein in InterPro IPR037596, Sec13 IPR037363, Sec13/Seh1_fam IPR015943, WD40/YVTN_repeat-like_dom_sf IPR001680, WD40_repeat IPR036322, WD40_repeat_dom_sf |
PANTHERi | PTHR11024, PTHR11024, 1 hit PTHR11024:SF2, PTHR11024:SF2, 1 hit |
Pfami | View protein in Pfam PF00400, WD40, 2 hits |
SMARTi | View protein in SMART SM00320, WD40, 6 hits |
SUPFAMi | SSF50978, SSF50978, 1 hit |
PROSITEi | View protein in PROSITE PS50082, WD_REPEATS_2, 3 hits PS50294, WD_REPEATS_REGION, 1 hit |
i Sequence
Sequence statusi: Complete.
10 20 30 40 50
MVVIANAHNE LIHDAVLDYY GKRLATCSSD KTIKIFEVEG ETHKLIDTLT
60 70 80 90 100
GHEGPVWRVD WAHPKFGTIL ASCSYDGKVL IWKEENGRWS QIAVHAVHSA
110 120 130 140 150
SVNSVQWAPH EYGPLLLVAS SDGKVSVVEF KENGTTSPII IDAHAIGVNS
160 170 180 190 200
ASWAPATIEE DGEHNGTKES RKFVTGGADN LVKIWKYNSD AQTYVLESTL
210 220 230 240 250
EGHSDWVRDV AWSPTVLLRS YLASVSQDRT CIIWTQDNEQ GPWKKTLLKE
260 270 280 290
EKFPDVLWRA SWSLSGNVLA LSGGDNKVTL WKENLEGKWE PAGEVHQ
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | L05929 Genomic DNA Translation: AAA35028.1 U14913 Genomic DNA Translation: AAB67426.1 BK006945 Genomic DNA Translation: DAA09525.1 |
PIRi | A45442 |
RefSeqi | NP_013309.1, NM_001182095.1 |
Genome annotation databases
EnsemblFungii | YLR208W_mRNA; YLR208W; YLR208W |
GeneIDi | 850905 |
KEGGi | sce:YLR208W |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | L05929 Genomic DNA Translation: AAA35028.1 U14913 Genomic DNA Translation: AAB67426.1 BK006945 Genomic DNA Translation: DAA09525.1 |
PIRi | A45442 |
RefSeqi | NP_013309.1, NM_001182095.1 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
2PM6 | X-ray | 2.45 | B/D | 1-297 | [»] | |
2PM7 | X-ray | 2.35 | B/D | 1-297 | [»] | |
2PM9 | X-ray | 3.30 | B | 1-297 | [»] | |
3IKO | X-ray | 3.20 | A/D/G | 1-297 | [»] | |
3JRO | X-ray | 4.00 | A | 1-297 | [»] | |
3JRP | X-ray | 2.60 | A | 1-297 | [»] | |
3MZK | X-ray | 2.69 | A/D | 1-297 | [»] | |
3MZL | X-ray | 2.80 | A/C/E/G | 1-297 | [»] | |
4BZJ | electron microscopy | 40.00 | B/F | 2-292 | [»] | |
4BZK | electron microscopy | 40.00 | B/F | 1-297 | [»] | |
4XMM | X-ray | 7.38 | A | 1-297 | [»] | |
4XMN | X-ray | 7.60 | A | 1-297 | [»] | |
6ZG5 | electron microscopy | 40.00 | B/F | 1-297 | [»] | |
6ZG6 | electron microscopy | 40.00 | B/D/F/H | 1-297 | [»] | |
6ZL0 | electron microscopy | 40.00 | B/D | 1-297 | [»] | |
SMRi | Q04491 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 31476, 301 interactors |
ComplexPortali | CPX-2523, COPII vesicle coat complex CPX-3231, SEA complex CPX-824, Nuclear pore complex |
DIPi | DIP-1826N |
IntActi | Q04491, 30 interactors |
MINTi | Q04491 |
STRINGi | 4932.YLR208W |
PTM databases
iPTMneti | Q04491 |
Proteomic databases
MaxQBi | Q04491 |
PaxDbi | Q04491 |
PRIDEi | Q04491 |
Genome annotation databases
EnsemblFungii | YLR208W_mRNA; YLR208W; YLR208W |
GeneIDi | 850905 |
KEGGi | sce:YLR208W |
Organism-specific databases
SGDi | S000004198, SEC13 |
VEuPathDBi | FungiDB:YLR208W |
Phylogenomic databases
eggNOGi | KOG1332, Eukaryota |
GeneTreei | ENSGT00940000153393 |
HOGENOMi | CLU_032441_0_1_1 |
InParanoidi | Q04491 |
OMAi | TVDTGHE |
Enzyme and pathway databases
Reactomei | R-SCE-204005, COPII-mediated vesicle transport R-SCE-3232142, SUMOylation of ubiquitinylation proteins R-SCE-4085377, SUMOylation of SUMOylation proteins R-SCE-4551638, SUMOylation of chromatin organization proteins R-SCE-4570464, SUMOylation of RNA binding proteins |
Miscellaneous databases
EvolutionaryTracei | Q04491 |
PROi | PR:Q04491 |
RNActi | Q04491, protein |
Family and domain databases
Gene3Di | 2.130.10.10, 1 hit |
InterProi | View protein in InterPro IPR037596, Sec13 IPR037363, Sec13/Seh1_fam IPR015943, WD40/YVTN_repeat-like_dom_sf IPR001680, WD40_repeat IPR036322, WD40_repeat_dom_sf |
PANTHERi | PTHR11024, PTHR11024, 1 hit PTHR11024:SF2, PTHR11024:SF2, 1 hit |
Pfami | View protein in Pfam PF00400, WD40, 2 hits |
SMARTi | View protein in SMART SM00320, WD40, 6 hits |
SUPFAMi | SSF50978, SSF50978, 1 hit |
PROSITEi | View protein in PROSITE PS50082, WD_REPEATS_2, 3 hits PS50294, WD_REPEATS_REGION, 1 hit |
MobiDBi | Search... |
Entry informationi
Entry namei | SEC13_YEAST | |
Accessioni | Q04491Primary (citable) accession number: Q04491 Secondary accession number(s): D6VYK9 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | October 1, 1993 |
Last sequence update: | October 1, 1993 | |
Last modified: | February 23, 2022 | |
This is version 200 of the entry and version 1 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Fungal Protein Annotation Program |
Miscellaneousi
Keywords - Technical termi
3D-structure, Direct protein sequencing, Reference proteomeDocuments
- Yeast
Yeast (Saccharomyces cerevisiae): entries, gene names and cross-references to SGD - Yeast chromosome XII
Yeast (Saccharomyces cerevisiae) chromosome XII: entries and gene names - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families